An ALignment
Editor based on GNU Emacs.

Can read and write alignments in GenBank, EMBL, Fast-A, and
Phylip formats, in addition to its own format, designed for speedy
access to large alignments;

Is free /
open source software. This means that Ale is distributed with
full source code, which you are guaranteed the right to modify and
redistribute. You can support and extend Ale in-house, if you
want.

Ale is built on top of
GNU Emacs, and
requires Emacs 24 or higher to run.

Screenshots

History

Ale was originally written in 1994-1995, as a project of the
laboratory of Prof. Carl Woese at the University of Illinois at
Urbana-Champaign and the laboratory of Prof. Norman Pace at the
University of Indiana, Bloomington. It then lay dormant for about
seven years, then perked up for a while, then went dormant again, then
perked up a little bit, and now might or might not be dormant. You
can download Ale here and try it out; if you run into any problems, or
are interested in continuing Ale development, please
contact Jim Blandy
or Karl Fogel.

Documentation

Quick Start

If you've just downloaded, built, and installed Ale, and now you're
wondering how to try it, run this from the top of the Ale source
tree:

ale demo-data/demo.gb

Other Similar Software

Ale isn't the only genetic sequence written in Emacs and released
as free software, believe it or not. There's
also RALEE (RNA
ALignment Editor in Emacs), by Sam Griffiths-Jones, which was
written up in Oxford University's journal Bioinformatics, vol. 21, issue 2.

Also, the Debian GNU/Linux
distribution lists a sequence editor called
biomode,
which mentions Emacs as a dependency.